Ministers and mandarins last night prepared for a showdown with trade union leaders after civil servants across five government departments voted to strike in the biggest Whitehall walkout for 13 years.

Tens of thousands of employees in jobcentres, courts, immigration and other services are to stage a two-day stoppage on Thursday and Friday next week in a series of pay disputes.

Government officials made it clear that Tony Blair's administration, which deployed troops to confront the vastly more powerful firefighters, would not "give in" to industrial action in the civil service.

Union leaders are planning a follow-up campaign of more limited disruption, including overtime bans and work-to-rules, and spreading the action to more groups, in what threatens to be a protracted confrontation.

Five separate postal ballots covering some 100,000 staff in work and pensions, constitutional affairs, Home Office, Prison Service and Treasury services triggered the strikes.

The government said turnouts were low at 31% to 48% but the union countered most were relatively high for postal ballots and well above the likely figure in June's European elections.

Mark Serwotka, general secretary of the Public and Commercial Services Union, by far the largest in the civil service, said the stereotypical image of Whitehall employees as "bowler-hatted Sir Humphreys on fat pay and a huge pension" was incorrect.

Nearly 15,000 earned less than £10,000 a year working full-time, he said, and 20,000 of those in the Department for Work and Pensions handling benefit claims qualified for the means-tested payments they administered.

"Strike action is the absolute last resort but we have tried for the past six months to end appalling low pay rates in the civil service and the time has come for something to be done," said Mr Serwotka.

The strike will be the most extensive in the civil service since a 1991 walkout over "market testing" and privatisation.

Union leaders claimed pay offers were worth between 0.5% and 2.8% but heads of the departments involved maintained they were much higher when performance awards were included.

Sir Richard Mottram, permanent secretary at the Department for Work and Pensions, the biggest caught up in the dispute, accused the union of misrepresenting its pay offer as 2.6% when, he insisted, more than half of staff would receive at least 5%.

One in four would gain between 7% and 8%, he added, and the 2.6% would apply to just 14% of the workers. It would be "indefensible", he said, if the workers went on strike over a "significant" offer. He conceded the department had underspent its budget by about £100m but that, he said, would be used to improve services.

A statement from the department said: "Despite union suggestions, the department does not have any more money available to spend on salaries. We have a challenging programme of work to help some of the most disadvantaged people in the UK and need to ensure taxpayers' money is spent responsibly.

"In these circumstances strike action is wholly inappropriate, but the DWP remains willing to talk to the union about the overall shape of the pay deal."

Mr Serwotka apologised in advance for any inconvenience to the public and urged users of the services not to take their frustration out on staff.

"The finger of blame should be pointed firmly at the government and these departments. We are sorry for any inconvenience the action will cause but there comes a point when you have to do something about poverty pay."

Public services face disruption next Thursday and Friday. England and Wales will be hit hardest, with industrial action in Scotland limited to jobcentres and benefit offices. Union leaders say the sectors involved are: